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## Citation
Mangiola et al., (2020). tidyHeatmap: an R package for modular heatmap production based on tidy principles. Journal of Open Source Software, 5(52), 2472, https://doi.org/10.21105/joss.02472

Please have a look also to 

- [tidygate](https://github.com/stemangiola/tidygate/) for adding custom gate information to your tibble 
- [tidySingleCellExperiment](https://stemangiola.github.io/tidySingleCellExperiment/) for tidy manipulation of Seurat objects
- [tidyseurat](https://stemangiola.github.io/tidyseurat/) for tidy manipulation of Seurat objects
- [tidybulk](https://stemangiola.github.io/tidybulk/) for tidy high-level data analysis and manipulation 
- [tidySummarizedExperiment](https://stemangiola.github.io/tidySummarizedExperiment/) for heatmaps produced with tidy principles

website: [stemangiola.github.io/tidyHeatmap](https://stemangiola.github.io/tidyHeatmap/)

`tidyHeatmap` is a package that introduces tidy principles to the creation of information-rich heatmaps. 
This package uses [ComplexHeatmap](https://bioconductor.org/packages/release/bioc/html/ComplexHeatmap.html) as graphical engine.

**Advantages:**

  - Modular annotation with just specifying column names
  - Custom grouping of rows is easy to specify providing a grouped tbl.
    For example `df |> group_by(...)`
  - Labels size adjusted by row and column total number
  - Default use of Brewer and Viridis palettes

## Functions/utilities available

Function | Description
------------ | -------------
`heatmap` | Plots base heatmap
`add_tile` | Adds tile annotation to the heatmap
`add_point` | Adds point annotation to the heatmap
`add_bar` | Adds bar annotation to the heatmap
`add_line` | Adds line annotation to the heatmap
`layer_point` | Adds layer of symbols on top of the heatmap
`layer_square` | Adds layer of symbols on top of the heatmap
`layer_diamond` | Adds layer of symbols on top of the heatmap
`layer_arrow_up` | Adds layer of symbols on top of the heatmap
`layer_arrow_down` | Add layer of symbols on top of the heatmap
`split_rows` | Splits the rows based on the dendogram
`split_columns` | Splits the columns based on the dendogram
`save_pdf` | Saves the PDF of the heatmap

## Installation

To install the most up-to-date version


```r
devtools::install_github("stemangiola/tidyHeatmap")
```


To install the most stable version (however please keep in mind that this package is under a maturing lifecycle stage)


```r
install.packages("tidyHeatmap")
```

## Contribution

If you want to contribute to the software, report issues or problems with the software or seek support please open an issue [here](https://github.com/stemangiola/tidyHeatmap/issues)

## Input data frame

The heatmaps visualise a multi-element, multi-feature dataset, annotated with independent variables. Each observation is a element-feature pair (e.g., person-physical characteristics).

element | feature | value | independent_variables
------------ | ------------- | ------------- | -------------
`chr` or `fctr` | `chr` or `fctr` | `numeric` | ...

Let's transform the mtcars dataset into a tidy "element-feature-independent variables" data frame. Where the independent variables in this case are 'hp' and 'vs'.












































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